diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 281 |
1 files changed, 214 insertions, 67 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c8ba314d38..41b60325d2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27,7 +27,7 @@ ;;; Copyright © 2016 Dylan Jeffers <sapientech@[email protected]> ;;; Copyright © 2016 David Craven <[email protected]> ;;; Copyright © 2016-2022 Marius Bakke <[email protected]> -;;; Copyright © 2016, 2017, 2021 Stefan Reichör <[email protected]> +;;; Copyright © 2016, 2017, 2021, 2022 Stefan Reichör <[email protected]> ;;; Copyright © 2016, 2017, 2019 Alex Vong <[email protected]> ;;; Copyright © 2016, 2017, 2018, 2021 Arun Isaac <[email protected]> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <[email protected]> @@ -2014,14 +2014,14 @@ class.") (define-public python-can (package (name "python-can") - (version "3.3.3") + (version "3.3.4") (source (origin (method url-fetch) (uri (pypi-uri "python-can" version)) (sha256 (base32 - "123lz1bl6xf3d0fvxzr4bg4884yg4m9s21z6xd2m68zhnbv9rmpc")))) + "0jclrvyxasaaxr0albq0kqrnrfqdgqxs7m2qw9nd8kfwg8xj4g1d")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -2030,7 +2030,8 @@ class.") (substitute* "setup.py" (("mock~=2\\.0") "mock") (("coverage<5") "coverage") - (("pytest~=4\\.3") "pytest") + (("pytest~=4\\.6") "pytest") + (("pytest-timeout~=1\\.3") "pytest-timeout") (("hypothesis~=4\\.56") "hypothesis")) #t)) (add-after 'unpack 'fix-broken-tests @@ -5075,7 +5076,7 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (define-public python-pydantic (package (name "python-pydantic") - (version "1.8.2") + (version "1.9.0") (source (origin (method git-fetch) @@ -5084,7 +5085,7 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "06162dss6mvi7wiy2lzxwvzajwxgy8b2fyym7qipaj7zibcqalq2")))) + (base32 "14wj3k9007fpbxk7593w6gdqrr68yzrsw4a41sj5ji4cv3r8z18b")))) (build-system python-build-system) (arguments '(#:phases @@ -5238,6 +5239,8 @@ matching of file paths.") (arguments `(#:phases (modify-phases %standard-phases + ;; XXX Remove this when updating this package: + ;; https://github.com/psf/black/issues/2703#issuecomment-1004752142 (add-after 'unpack 'relax-version-requirements (lambda _ (substitute* "setup.py" @@ -5829,12 +5832,13 @@ readable format.") ("pkg-config" ,pkg-config) ("python-sphinx" ,python-sphinx) ("python-numpydoc" ,python-numpydoc) - ("texlive" ,(texlive-updmap.cfg (list texlive-cm-super + ("texlive" ,(texlive-updmap.cfg (list + texlive-capt-of + texlive-cm-super texlive-fonts-ec texlive-generic-iftex texlive-pdftex texlive-amsfonts - texlive-latex-capt-of texlive-latex-cmap texlive-latex-environ texlive-latex-eqparbox @@ -6543,19 +6547,19 @@ toolkits.") ("python-mock" ,python-mock) ("graphviz" ,graphviz) ("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts - texlive-latex-amsmath - texlive-latex-enumitem - texlive-latex-expdlist - texlive-latex-geometry - texlive-latex-preview - texlive-latex-type1cm - texlive-latex-ucs - - texlive-pdftex - - texlive-fonts-ec - texlive-times - texlive-txfonts))) + texlive-enumitem + texlive-latex-amsmath + texlive-latex-expdlist + texlive-latex-geometry + texlive-latex-preview + texlive-latex-type1cm + texlive-latex-ucs + + texlive-pdftex + + texlive-fonts-ec + texlive-times + texlive-txfonts))) ("texinfo" ,texinfo) ,@(package-native-inputs python-matplotlib))) (arguments @@ -7910,7 +7914,7 @@ cluster without needing to write any wrapper code yourself.") (define-public python-honcho (package (name "python-honcho") - (version "1.0.1") + (version "1.1.0") (source (origin (method git-fetch) @@ -7919,7 +7923,7 @@ cluster without needing to write any wrapper code yourself.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "11bd87474qpif20xdcn0ra1idj5k16ka51i658wfpxwc6nzsn92b")))) + (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj")))) (build-system python-build-system) (native-inputs (list python-pytest python-mock python-tox which)) ;for tests @@ -7938,7 +7942,8 @@ cluster without needing to write any wrapper code yourself.") ;; It's easier to run tests after install. ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) - (invoke "py.test" "-v")))))) + ;; Skip failing test_export + (invoke "py.test" "-v" "-k" "not test_export")))))) (home-page "https://github.com/nickstenning/honcho") (synopsis "Manage Procfile-based applications") (description @@ -8238,6 +8243,15 @@ need to use the older and less efficient @code{pkg_resources} package.") (base32 "1n7qxa1snj06aw45mcfz7bxc46zp7fxj687140g2k6jcnyjmfxrz")))) (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-pytest)) (home-page "https://github.com/alecthomas/importmagic") (synopsis "Library for adding, removing and managing Python imports") (description @@ -8869,6 +8883,7 @@ callback signature using a prototype function.") Powerful interactive shells, a browser-based notebook, support for interactive data visualization, embeddable interpreters and tools for parallel computing.") + (properties '((cpe-name . "ipython"))) (license license:bsd-3))) (define-public python-ipython-documentation @@ -8916,10 +8931,10 @@ computing.") ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) ;; FIXME: It's possible that a smaller union would work just as well. ("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts + texlive-capt-of texlive-fonts-ec texlive-generic-iftex texlive-pdftex - texlive-latex-capt-of texlive-latex-cmap texlive-latex-environ texlive-latex-eqparbox @@ -9612,11 +9627,28 @@ SVG, EPS, PNG and terminal output.") (uri (pypi-uri "seaborn" version)) (sha256 (base32 "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) - (patches (search-patches "python-seaborn-kde-test.patch")))) + (patches (search-patches "python-seaborn-kde-test.patch" + "python-seaborn-2690.patch")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-more-tests + (lambda _ + (substitute* "seaborn/tests/test_distributions.py" + (("get_contour_color\\(ax\\.collections\\[0\\]\\)") + "get_contour_color(ax.collections[0])") + (("c\\.get_color\\(\\)") "get_contour_color(c)") + + ;; These three are borked and have been fixed upstream, but + ;; there's no simple patch we could apply here, so we just + ;; disable them. + (("def test_hue_ignores_cmap") + "def skip_test_hue_ignores_cmap") + (("def test_fill_artists") + "def skip_test_fill_artists") + (("def test_with_rug") + "def skip_test_with_rug")))) (add-before 'check 'start-xserver (lambda _ ;; There must be a running X server and make check doesn't @@ -11085,30 +11117,23 @@ third-party code.") (define-public python-llfuse (package (name "python-llfuse") - (version "1.3.8") + (version "1.4.1") (source (origin (method url-fetch) (uri (pypi-uri "llfuse" version)) (sha256 (base32 - "1g2cdhdqrb6m7655qp61pn61pwj1ql61cdzhr2jvl3w4i8877ddr")))) + "1jaf790rsxvz3hs9fbr3hrnmg0xzl6a2bqfa10bbbsjsdbcpk762")))) (build-system python-build-system) (inputs (list fuse attr)) (native-inputs - (list pkg-config)) + (list pkg-config python-pytest)) (synopsis "Python bindings for FUSE") (description "Python-LLFUSE is a set of Python bindings for the low level FUSE API.") (home-page "https://bitbucket.org/nikratio/python-llfuse/") - (license license:lgpl2.0+) - (properties `((python2-variant . ,(delay python2-llfuse)))))) - -(define-public python2-llfuse - (let ((base (package-with-python2 - (strip-python2-variant python-llfuse)))) - (package/inherit base - (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2)))))) + (license license:lgpl2.0+))) (define-public python-msgpack (package @@ -11416,6 +11441,32 @@ Unicode-aware. It is not intended as an end-user tool.") (define-public python2-xlrd (package-with-python2 python-xlrd)) +;; We need this for python-anndata +(define-public python-xlrd-1 + (package + (inherit python-xlrd) + (name "python-xlrd") + (version "1.2.0") + (source (origin + ;; The tests are not included in the PyPI archive. + (method git-fetch) + (uri (git-reference + (url "https://github.com/python-excel/xlrd") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sm5p0ii5ayh52ak1jpw0n1kgsv72vdwwp8c3z13l8yf4irsb587")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Some tests depend on writing a temporary file to the user's home + ;; directory. + (add-after 'unpack 'fix-tests + (lambda _ + (setenv "HOME" "/tmp")))))))) + ;;; Note: this package is unmaintained since 2018 (archived on GitHub). (define-public python-xlwt (package @@ -11641,6 +11692,73 @@ asyncio.") Python code formatter \"black\".") (license license:expat))) +(define-public python-geojson + (package + (name "python-geojson") + (version "2.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "geojson" version)) + (sha256 + (base32 "12k5bzqskvq3gqzkryarhdjl0df47y5k9cf8r3clasi2wjnbfjvf")))) + (build-system python-build-system) + (arguments + ;; https://github.com/jazzband/geojson/issues/175 + `(#:tests? #f)) + (home-page "https://github.com/jazzband/geojson") + (synopsis "Python bindings and utilities for GeoJSON") + (description + "This package provides Python bindings and utilities for +@uref{http://geojson.org/, GeoJSON}, a format for encoding geographic data +structures.") + (license license:bsd-3))) + +(define-public wfetch + (let ((commit "e1cfa37814aebc9eb56ce994ebe877b6a6f9a715") + (revision "1")) + (package + (name "wfetch") + (version (git-version "0.1-pre" revision commit)) + (home-page "https://github.com/Gcat101/Wfetch") + (source + (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dmr85plx8zr6s14ym3r32g6crwxghkval5a24ah90ijx4dbn5q5")))) + (build-system python-build-system) + (arguments + `(#:use-setuptools? #f ; no setup.py + #:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share"))) + (mkdir-p share) + (substitute* "wfetch/wfetch.py" + (("os.sep, 'opt', 'wfetch'") (string-append "'" share "'"))) + (install-file "wfetch/wfetch.py" bin) + (copy-recursively "wfetch/icons" share))))))) + (inputs (list python-pyowm python-fire python-termcolor python-requests)) + (synopsis "Command-line tool to display weather info") + (description + "This package provides a tool similar to Neofetch/pfetch, but for +weather: it can display the weather condition, temperature, humidity, etc. + +To use it, you must first run: + +@example +export WEATHER_CLI_API=@var{your OpenWeatherMap API key} +@end example\n") + (license license:gpl3+)))) + (define-public python-get-version (package (name "python-get-version") @@ -11941,17 +12059,6 @@ the Python standard library but currently only supports the older 2003 specification.") (license license:bsd-4))) -(define-public python-idna-2.7 - (package (inherit python-idna) - (version "2.7") - (source (origin - (method url-fetch) - (uri (pypi-uri "idna" version)) - (sha256 - (base32 - "05jam7d31767dr12x0rbvvs8lxnpb1mhdb2zdlfxgh83z6k3hjk8")))))) - - (define-public python2-idna (package-with-python2 python-idna)) @@ -11971,17 +12078,27 @@ specification.") (base32 "1r0kgl7i6nnhgjl44sjw57k08gh2qr7l8slqih550dyxbf1akbxh")))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases ;; Use Guix package of libsass instead of compiling from a checkout. (add-before 'build 'set-libsass - (lambda _ - (setenv "SYSTEM_SASS" (assoc-ref %build-inputs "libsass")) - #t)) + (lambda _ (setenv "SYSTEM_SASS" "indeed"))) (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "sasstests.py")))) + (add-after 'install 'delete-test (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "sasstests.py")))))) + ;; Delete sasstests.py because it attempts to open a file + ;; that is not installed when loaded, which breaks the sanity + ;; check. + (delete-file (string-append + (assoc-ref outputs "out") + "/lib/python" + (python-version + (dirname (dirname + (search-input-file inputs "bin/python")))) + "/site-packages/sasstests.py"))))))) (native-inputs (list python-pytest python-werkzeug)) (inputs @@ -12611,13 +12728,12 @@ time.") texlive-amsfonts texlive-booktabs texlive-caption + texlive-enumitem texlive-eurosym texlive-fonts-rsfs - texlive-generic-ulem texlive-generic-iftex texlive-jknappen texlive-latex-amsmath - texlive-latex-enumitem texlive-latex-fancyvrb texlive-latex-float texlive-fontspec @@ -12637,6 +12753,7 @@ time.") texlive-tcolorbox texlive-titling texlive-tools + texlive-ulem texlive-xcolor texlive-zapfding))))) (propagated-inputs @@ -15380,9 +15497,8 @@ CloudFront content delivery network.") ;; Hard-code the path to pkg-config. (lambda _ (substitute* "pkgconfig/pkgconfig.py" - (("cmd = 'pkg-config") - (string-append "cmd = '" (which "pkg-config")))) - #t)) + (("'pkg-config'") + (string-append "'" (which "pkg-config") "'"))))) (replace 'check (lambda _ (invoke "nosetests" "test.py")))))) @@ -19137,7 +19253,12 @@ multitouch applications.") ;; TypeError: parse() missing 2 required positional arguments: 'tree' and ;; 'parse_funcs' ;; during test setup. - `(#:tests? #f)) + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + ;; translate-toolkit has many optional dependencies (see + ;; optional.txt), which the sanity check does not understand. + (delete 'sanity-check)))) (home-page "https://toolkit.translatehouse.org") (synopsis "Tools and API for translation and localization engineering") (description @@ -21697,7 +21818,12 @@ working with iterables.") (inputs (list python-latexcodec python-pyyaml python-six)) (arguments - `(#:test-target "nosetests")) + (list + #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "nosetests"))))))) (home-page "https://pybtex.org/") (synopsis "BibTeX-compatible bibliography processor") (description "Pybtex is a BibTeX-compatible bibliography processor written @@ -22632,7 +22758,7 @@ N-dimensional arrays for Python.") (define-public python-anndata (package (name "python-anndata") - (version "0.7.6") + (version "0.7.8") (source (origin ;; The tarball from PyPi doesn't include tests. @@ -22643,7 +22769,7 @@ N-dimensional arrays for Python.") (file-name (git-file-name name version)) (sha256 (base32 - "1q30bsfsq9xfqm8nmabg3bjh9gix3yng0170xiiyw1lin4xncf0q")))) + "1rrr9xfdaf00ixj5gyym75bl78gkaj55yfw3wjhvx0pdwqpwp9py")))) (build-system python-build-system) (arguments `(#:phases @@ -22658,6 +22784,9 @@ N-dimensional arrays for Python.") (replace 'build (lambda _ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) + (substitute* "anndata/_metadata.py" + (("__version__ =.*") + (string-append "__version__ = \"" ,version "\"\n"))) ;; ZIP does not support timestamps before 1980. (setenv "SOURCE_DATE_EPOCH" "315532800") (invoke "flit" "build"))) @@ -22669,8 +22798,7 @@ N-dimensional arrays for Python.") (format #true wheel) (invoke "python" "-m" "pip" "install" wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$"))) - #t))))) + (find-files "dist" "\\.whl$")))))))) (propagated-inputs (list python-h5py python-importlib-metadata @@ -22679,6 +22807,7 @@ N-dimensional arrays for Python.") python-packaging python-pandas python-scipy + python-xlrd-1 python-zarr)) (native-inputs (list python-joblib python-pytest python-toml python-flit @@ -28088,13 +28217,13 @@ spreadsheet), CSV, TSV, XLS, XLSX (Microsoft Excel spreadsheet), and YAML.") (define-public python-febelfin-coda (package (name "python-febelfin-coda") - (version "0.1.0") + (version "0.2.0") (source (origin (method url-fetch) (uri (pypi-uri "febelfin-coda" version)) (sha256 - (base32 "10nf4hdwldqgdmh4g613vx55sbsw1x1yzpvs3crwlggbp75fjjfi")))) + (base32 "1isnf87gxlvfbmackv7b2c978vmnj7ij0v4svhyjl8pbb9hwjsvm")))) (build-system python-build-system) (home-page "https://coda.b2ck.com/") (synopsis "Module to parse Belgian CODA files") @@ -28786,3 +28915,21 @@ but not binary streams.") "This package provides ECMAScript parsing infrastructure for multipurpose analysis in Python.") (license license:bsd-3))) + +(define-public python-types-dataclasses + (package + (name "python-types-dataclasses") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "types-dataclasses" version)) + (sha256 + (base32 + "1mq6qd365m8ml889zl5dxj9kncjv71iq1d1fvgj59y0ixlpm6s35")))) + (build-system python-build-system) + (home-page "https://github.com/python/typeshed") + (synopsis "Typing stubs for dataclasses") + (description + "This packages provides a collection of library stubs for Python, with +static types.") + (license license:asl2.0))) |